After playing twice for Yugoslavia in 1991, Stanić won 49 international caps and scored seven goals for the Croatia national team between 1995 and 2003,[4] making his international debut in a UEFA Euro 1996 qualifying against Estonia in September 1995. He made three appearances for Croatia at the Euro 1996 finals in England and went on to appear in all of the team's seven matches at the 1998 FIFA World Cup finals in France, where they won the bronze medal. At the latter tournament, he scored Croatia's first-ever World Cup goal in their opening 3–1 victory over Jamaica and assisted in Robert Jarni's opening goal in their 3–0 victory over Germany in the quarterfinals. Stanić also made two appearances for Croatia at the 2002 FIFA World Cup finals as a second-half substitute, only to see Croatia fall short of qualifying for the second round of the tournament. His last international appearance came in April 2003 as a half-time substitute in a friendly match against Sweden.[5]
He was forced to retire at the age of 32 after developing a serious knee injury during the 2003–04 league season.